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Original Investigation
October 15, 2020

Site-Specific and Targeted Therapy Based on Molecular Profiling by Next-Generation Sequencing for Cancer of Unknown Primary Site: A Nonrandomized Phase 2 Clinical Trial

Author Affiliations
  • 1Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
  • 2Department of Medical Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
  • 3Division of Medical Oncology/Hematology, Kobe University Graduate School of Medicine, Kobe, Japan
  • 4Department of Medical Oncology, Osaka City General Hospital, Osaka, Japan
  • 5Department of Medical Oncology, International Medical Center, Saitama Medical University, Hidaka, Japan
  • 6Third Department of Internal Medicine, Wakayama Medical University, Wakayama, Japan
  • 7Department of Medical Oncology, Hiroshima City Hospital Organization, Hiroshima City Hiroshima Citizens Hospital, Hiroshima, Japan
  • 8Department of Medical Oncology, Toranomon Hospital, Tokyo, Japan
  • 9Medical Oncology Division, Hyogo Cancer Center, Akashi, Japan
  • 10Department of Medical Oncology, Tohoku University Hospital, Sendai, Japan
  • 11Department of Medical Oncology, Kobe City Medical Center General Hospital, Kobe, Japan
  • 12Department of Respiratory Medicine and Medical Oncology, Gifu Municipal Hospital, Gifu, Japan
  • 13Division of Clinical Oncology, Shizuoka Cancer Center, Shizuoka, Japan
  • 14Clinical Research Center, Kindai University Hospital, Osaka-Sayama, Japan
  • 15Chiba Cancer Center, Research Institute, Chiba, Japan
  • 16Department of Genome Biology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
  • 17Center for Comprehensive Genomic Medicine, Okayama University Hospital, Okayama, Japan
JAMA Oncol. Published online October 15, 2020. doi:10.1001/jamaoncol.2020.4643
Key Points

Question  Does site-specific treatment, including molecularly targeted therapy based on profiling gene expression and gene alterations by next-generation sequencing, have clinical use for patients with cancer of unknown primary site?

Findings  This phase 2 nonrandomized clinical trial of such site-specific treatment in 97 patients with cancer of unknown primary site revealed a 1-year survival probability of 53.1%, with a durable response to targeted therapy being observed in patients with actionable genetic alterations.

Meaning  Site-specific treatment, including guided targeted therapy based on next-generation sequencing, is a promising strategy for patients with cancer of unknown primary site and warrants further investigation in a randomized clinical trial.


Importance  Although profiling of gene expression and gene alterations by next-generation sequencing (NGS) to predict the primary tumor site and guide molecularly targeted therapy might be expected to improve clinical outcomes for cancer of unknown primary site (CUP), to our knowledge, no clinical trial has previously evaluated this approach.

Objective  To assess the clinical use of site-specific treatment, including molecularly targeted therapy based on NGS results, for patients with CUP.

Design, Setting, and Participants  This phase 2 clinical trial was conducted at 19 institutions in Japan and enrolled 111 previously untreated patients with the unfavorable subset of CUP between March 2015 and January 2018, with 97 patients being included in the efficacy analysis. Eligibility criteria included a diagnosis of unfavorable CUP after mandatory examinations, including pathological evaluation by immunohistochemistry, chest-abdomen-pelvis computed tomography scans, and a positron emission tomography scan.

Interventions  RNA and DNA sequencing for selected genes was performed simultaneously to evaluate gene expression and gene alterations, respectively. A newly established algorithm was applied to predict tumor origin based on these data. Patients received site-specific therapy, including molecularly targeted therapy, according to the predicted site and detected gene alterations.

Main Outcomes And Measures  The primary end point was 1-year survival probability. Secondary end points included progression-free survival (PFS), overall survival (OS), objective response rate, safety, efficacy according to predicted site, and frequency of gene alterations.

Results  Of 97 participants, 49 (50.5%) were women and the median (range) age was 64 (21-81) years. The cancer types most commonly predicted were lung (21 [21%]), liver (15 [15%]), kidney (15 [15%]), and colorectal (12 [12%]) cancer. The most frequent gene alterations were in TP53 (45 [46.4%]), KRAS (19 [19.6%]), and CDKN2A (18 [18.6%]). The 1-year survival probability, median OS, and median PFS were 53.1% (95% CI, 42.6%-62.5%), 13.7 months (95% CI, 9.3-19.7 months), and 5.2 months (95% CI, 3.3-7.1 months), respectively. Targetable EGFR mutations in tumor specimens were detected in 5 patients with predicted non–small-cell lung cancer (5.2%), 4 of whom were treated with afatinib; 2 of these patients achieved a durable PFS of longer than 6 months.

Conclusions and Relevance  This study’s findings suggest that site-specific treatment, including molecularly targeted therapy based on profiling gene expression and gene alterations by NGS, can contribute to treating patients with the unfavorable subset of CUP.

Trial Registration  UMIN Identifier: UMIN000016794

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